SIBO & IBS Treatment


Without a doubt, one of the most common conditions I see in my practice is IBS or irritable bowel syndrome. It has become so common that it is estimated to be the second leading cause for missing work in the US and costs the government 30 billion dollars per year (1). 


Equally staggering is that 60% if these patients suffer from a condition called SIBO (small intestinal bacterial overgrowth).  


Functional Medicine vs. Conventional Medicine


Whilst conventional medicine focuses mainly on managing the symptoms of IBS and SIBO, a functional medicine approach aims to uncover the underlying root cause. For many IBS patients, SIBO may be a very important underlying factor which, when treated, can result in the resolution or improvement of symptoms to the point where pharmacotherapy for IBS is no longer needed.


This functional medicine approach looks slightly different for each patient, depending on their genetics, epigenetics, lifestyle, diet, environmental factors, and biochemical markers.  However, for most patients a few key components form part of an effective management plan:


The Functional Medicine IBS/SIBO Treatment


Functional Medicine treats IBS and SIBO by implementing the following 6 practices. Doing these will optimize gut flora and overall gut health.


1. Optimizing the function of the Vagus Nerve and Migrating Motor Complex

A functioning vagus nerve seems an insignificant component but makes all the difference in preventing recurrence of SIBO. The Vagus nerve and migrating motor complex form part of the central and enteric (intestinal) nervous systems. These are largely responsible for regulating the intestinal transit time so to speak. Ensuring that our bowel content is making its journey in a timely way is imperative to achieving and maintaining a healthy bacterial balance in the gut. Using a prescribed motility agent, practicing intermittent fasting, doing breathwork, mindfulness, meditation and yoga have all been clinically proven to help optimize the function of the Vagus nerve and the MMC (2).


I have witnessed my patients achieving long term SIBO eradication over and over again. These patients are the ones that put time and effort into supporting this functional system.


2. Diet

The majority of my SIBO patients show rapid improvement when guided through a two-staged therapeutic diet.  We initially remove foods high in Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyol.  I then transition them to a plan tailored to their individual food sensitivity results, whether they have associated co-infections (such as SIFO), all whilst addressing their nutritious, metabolic, and immune-related needs.


3. Supporting digestive enzymes and using food/nutrients to repair intestinal tight junctions

Having the right level of acidity and the appropriate presence of bile in the upper digestive tract plays a key role in eradicating unwanted bacteria.  It is not advisable to take digestive enzymes without seeking professional advice. Having a comprehensive stool analysis done will assist your functional medicine provider in advising you on how to optimize your digestive enzymes.


4. Anti-microbial (with or without anti-fungal) treatment 

Many different treatment protocols (pharmaceutical and botanical) are used to treat SIBO and /or SIFO (small intestinal fungal overgrowth).  Looking at your underlying antecedents, triggers and mediators helps me determine which regimen is right for you.


5. Probiotics

A careful choice of probiotic can go a long way to help eradicate the bacterial overgrowth in the small intestine.  It also helps to maintain healthy, balanced colonies of beneficial bacteria in the large intestine and prevent the recurrence of SIBO.


6. Other treatments

Intravenous gut-healing formulas, diatomaceous earth, biofilm disruptors, and fecal transplants are some of the other approaches we’ve used successfully in treating selected patients with refractory / non-responsive SIBO. 


SIBO continues to be one of the most challenging conditions to manage. Traditional treatment efficacy rates are low and recurrence rates are high.  If you suspect that you have SIBO and need experienced help in finding the right treatment plan, the team at Linden & Arc Vitality Institute can help you find that plan. Contact them today for a consultation.



1. Grace E., et al. (2013). Small intestinal bacterial overgrowth – prevalence, clinical features, current and developing diagnostic tests, and treatment. Alimentary Pharmacology and Therapeutics.

2. Umesh Pal Singh, Subharti Medical College, Meerut, Uttar Pradesh, India. Evidence-Based Role of Hypercapnia and Exhalation Phase in Vagus Nerve Stimulation: Insights into Hypercapnic Yoga Breathing Exercises.  Journal of Yoga and Physical Exercise ISSN: 2157-7595.Published Date: Oct 25, 2017